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Title: Recent advances in 16S rRNA gene-based phytoplasma differentiation, classification and taxonomy

Author
item Zhao, Yan
item WEI, WEI - University Of Maryland
item Davis, Robert
item Lee, Ing Ming

Submitted to: Phytoplasmas: Genomes, Plant Hosts and Vectors
Publication Type: Book / Chapter
Publication Acceptance Date: 4/29/2009
Publication Date: 1/15/2010
Citation: Zhao, Y., Wei, W., Davis, R.E., Lee, I. 2010. Recent advances in 16S rRNA gene-based phytoplasma differentiation, classification and taxonomy. In: Weintraub, P., Jones, P., editors. Phytoplasmas: Genomes, Plant Hosts and Vector. Wallingford, UK: CABI Publishing. p. 64-92.

Interpretive Summary:

Technical Abstract: Phytoplasmas are non-helical, mycoplasma-like cell wall-less bacteria known to be pathogenic to more than a thousand plant species. Due to the inability to cultivate phytoplasmas in cell-free media and the consequent inaccessibility of measurable phenotypic characters suitable for polyphasic characterizations, molecular analyses of conserved gene sequences have become primary means for phytoplasma taxonomy and classification. Genes encoding 16S ribosomal RNAs (16S rDNA) are highly conserved across the phytoplasma clade yet contain ample information for differentiation of diverse phytoplasma strains, therefore, have served as a major molecular tool for phytoplasma identification, genotyping, taxonomic assignment, and group/subgroup classification. Thus far, 28 ‘Candidatus Phytoplasma’ species have been formally described and 15 additional strains have been recognized as potentially new ‘Ca. Phytoplasma’ species based on their 16S rDNA sequences. Establishment of a pragmatic group/subgroup phytoplasma classification system based on restriction fragment length polymorphism (RFLP) analysis of 16S rDNA sequences has greatly facilitated differentiation of a broad array of phytoplasmas. With the recent updates and computer simulated RFLP pattern analysis, the 16S rDNA RFLP-based classification system has delineated a total of 30 phytoplasma groups and more than a hundred subgroups. An interactive Internet tool, iPhyClassifier, has been developed to conduct 16S rDNA sequence-based phytoplasma taxonomic assignment and group/subgroup classification online. Sophisticated molecular approaches such as oligonucleotide microarray, single-strand conformation polymorphism analysis, and quantitative real-time PCR have been applied to lineage- and strain-specific phytoplasma detections. These recent advances have extended our knowledge on the breadth of the genetic diversity and the dynamic and complex population structures of phytoplasmas.